Data processing methods and data acquisition for samples larger than the field of view in parallel-beam tomography

Discorpy: algorithms and software for camera calibration and correction

Camera or lens-based detector calibration is essential for spatial accuracy in applications like dimensional tomography, optical metrology, and computer vision. Many methods and software exist yet there is still a lack of approaches that achieve both high accuracy and robustness while being easy to use and capable of handling a wide range of distortions. Radial lens distortion is common in high-resolution X-ray detector optics used in parallel-beam tomography at synchrotrons. Achieving sub-pixel accuracy requires calibrating with an optical target image. Although methods for characterizing radial distortion are well established, acquired images often also include perspective distortion and optical center offset. Here, we present our approaches to individually characterize and correct both types of distortion using a single calibration image, implemented in the Discorpy software.

Synchrotron Radiation-Based Tomography of an Entire Mouse Brain with Sub-Micron Voxels: Augmenting Interactive Brain Atlases with Terabyte Data

Synchrotron radiation-based X-ray microtomography is uniquely suited for post-mortem 3D visualization of organs such as the mouse brain. Tomographic imaging of the entire mouse brain with isotropic cellular resolution requires an extended field-of-view and produces datasets of multiple terabytes in size. These data must be reconstructed, analyzed, and made accessible to domain experts who may have limited image processing knowledge. Extended-field X-ray microtomography is presented with0.65 μ m $0.65 \,\umu \mathrm{m}$ voxel size covering an entire mouse brain. The 4495 projections from 8 × 8 offset acquisitions are stitched to reconstruct a volume of 150003 voxels. The microtomography volume was non-rigidly registered to the Allen Mouse Brain Common Coordinate Framework v3 based on a combination of image intensity and landmark pairs. The data were block-wise transformed and stored in a public repository with a hierarchical format for navigation and overlay with anatomical annotations in online viewers such as Neuroglancer or siibra-explorer. This study demonstrates X-ray imaging and data processing for a full mouse brain, augmenting current atlases by improving resolution in the third dimension by an order of magnitude. The 3.3-teravoxel dataset is publicly available and easily accessible for domain experts via browser-based viewers.

Deciphering the Evolution of Current Distribution in Hybrid Silver Vanadium Oxide / Carbon Monofluoride Cathodes within Lithium Primary Batteries

For batteries to function effectively all active material must be accessible requiring both electron and ion transport to each particle. A common approach to generating the needed conductive network is the addition of carbon to create a composite electrode. An alternative approach is the electrochemically induced formation of conductive reaction products where the electrochemically generated materials are in intimate contact with the active material contributing to effective connection of each active particle. This study probes silver vanadium oxide (Ag2V4O11, SVO), carbon monofluoride (CFx), and hybrid SVO/CFx electrodes in lithium batteries. Ex situ XRD identifies Ag0 as a reduction product from SVO and LiF from CFx that can be followed as a function of depth-of-discharge (DOD). Spatially-resolved operando energy dispersive x-ray diffraction reveals that the presence of SVO alleviates reaction heterogeneity in the electrodes which are electron transfer limited in the absence of sufficient Ag0. Synchrotron X-ray tomography on discharged cathodes reveals the distribution of silver particles where the particles are more closely spaced near the current collector indicating multiple nucleation sites for their formation. Finally, operando isothermal microcalorimetry is used to determine the heat dissipation of the parent and hybrid battery types. Using material enthalpy potentials, we determine the current distribution between the two active materials for the discharging hybrid cathode adding further insight to the diffraction analysis. Taken together, these results provide a comprehensive understanding of hybrid SVO/CFx cathodes and give guidance on optimal compositions that balance power and energy density considerations.

Elucidating the Discharge Behavior of Aqueous Zinc Sulfur Batteries in the Presence of Molybdenum(IV) Chalcogenide Catalyst: The Criticality of Interfacial Electrochemistry

The aqueous zinc-sulfur battery holds promise for significant capacity and energy density with low cost and safe operation based on environmentally benign materials. However, it suffers from the sluggish kinetics of the conversion reaction. Here, we highlight the efficacy of molybdenum(IV) sulfide (MoS2) to reduce the overpotential of S-ZnS conversion in aqueous electrolytes and study the discharge products formed at the solid-solid and solid-liquid interfaces using experimental and theoretical approaches. Specifically, the MoS2-catalyzed electrochemical conversion reaction is characterized via ex situ X-ray diffraction (XRD), transmission electron microscopy (TEM) with energy dispersive spectroscopy (EDS), Raman spectroscopy, synchrotron-based Mo K-edge X-ray absorption spectroscopy (XAS), and in situ synchrotron-based X-ray computed tomography (XCT). Additionally, operando synchrotron-based S K-edge XAS and X-ray fluorescence (XRF) maps are collected to determine the spatial evolution of sulfur-based species at the electrode-electrolyte interface. Coupling the operando S K-edge XAS data with the simulated spectra and fitting the data suggested a possible ZnS2 intermediate phase.

Porous Iron Electrodes Reduce Energy Consumption During Electrocoagulation of a Virus Surrogate: Insights into Performance Enhancements Using Three-Dimensional Neutron Computed Tomography

Electrocoagulation has attracted significant attention as an alternative to conventional chemical coagulation because it is capable of removing a wide range of contaminants and has several potential advantages. In contrast to most electrocoagulation research that has been performed with nonporous electrodes, in this study, we demonstrate energy-efficient iron electrocoagulation using porous electrodes. In batch operation, investigation of the external pore structures through optical microscopy suggested that a low porosity electrode with sparse connection between pores may lead to mechanical failure of the pore network during electrolysis, whereas a high porosity electrode is vulnerable to pore clogging. Electrodes with intermediate porosity, instead, only suffered a moderate surface deposition, leading to electrical energy savings of 21% and 36% in terms of electrocoagulant delivery and unit log virus reduction, respectively. Neutron computed tomography revealed the critical role of electrode porosity in utilizing the electrode's internal surface for electrodissolution and effective delivery of electrocoagulant to the bulk. Energy savings of up to 88% in short-term operation were obtained with porous electrodes in a continuous flow-through system. Further investigation on the impact of current density and porosity in long-term operation is desired as well as the capital cost of porous electrodes.

Spexwavepy: an open-source Python package for X-ray wavefront sensing using speckle-based techniques

In situ wavefront sensing plays a critical role in the delivery of high-quality beams for X-ray experiments. X-ray speckle-based techniques stand out among other in situ techniques for their easy experimental setup and various data acquisition modes. Although X-ray speckle-based techniques have been under development for more than a decade, there are still no user-friendly software packages for new researchers to begin with. Here, we present an open-source Python package, spexwavepy, for X-ray wavefront sensing using speckle-based techniques. This Python package covers a variety of X-ray speckle-based techniques, provides plenty of examples with real experimental data and offers detailed online documentation for users. We hope it can help new researchers learn and apply the speckle-based techniques for X-ray wavefront sensing to synchrotron radiation and X-ray free-electron laser beamlines.

Mapping of lithium ion concentrations in 3D structures through development of in situ correlative imaging of X-ray Compton scattering-computed tomography

Understanding the correlation between chemical and microstructural properties is critical for unraveling the fundamental relationship between materials chemistry and physical structures that can benefit materials science and engineering. Here, we demonstrate novel in situ correlative imaging of the X-ray Compton scattering computed tomography (XCS-CT) technique for studying this fundamental relationship. XCS-CT can image light elements that do not usually exhibit strong signals using other X-ray characterization techniques. This paper describes the XCS-CT setup and data analysis method for calculating the valence electron momentum density and lithium-ion concentration, and provides two examples of spatially and temporally resolved chemical properties inside batteries in 3D. XCS-CT was applied to study two types of rechargeable lithium batteries in standard coin cell casings: (1) a lithium-ion battery containing a cathode of bespoke microstructure and liquid electrolyte, and (2) a solid-state battery containing a solid-polymer electrolyte. The XCS-CT technique is beneficial to a wide variety of materials and systems to map chemical composition changes in 3D structures.

TomoPyUI: a user-friendly tool for rapid tomography alignment and reconstruction

The management and processing of synchrotron and neutron computed tomography data can be a complex, labor-intensive and unstructured process. Users devote substantial time to both manually processing their data (i.e. organizing data/metadata, applying image filters etc.) and waiting for the computation of iterative alignment and reconstruction algorithms to finish. In this work, we present a solution to these problems: TomoPyUI, a user interface for the well known tomography data processing package TomoPy. This highly visual Python software package guides the user through the tomography processing pipeline from data import, preprocessing, alignment and finally to 3D volume reconstruction. The TomoPyUI systematic intermediate data and metadata storage system improves organization, and the inspection and manipulation tools (built within the application) help to avoid interrupted workflows. Notably, TomoPyUI operates entirely within a Jupyter environment. Herein, we provide a summary of these key features of TomoPyUI, along with an overview of the tomography processing pipeline, a discussion of the landscape of existing tomography processing software and the purpose of TomoPyUI, and a demonstration of its capabilities for real tomography data collected at SSRL beamline 6-2c.

Adaptive automated sinogram normalization for ring artifacts suppression in CT

Ring artifacts pose a major barrier to obtaining precise reconstruction in computed tomography (CT). The presence of ring artifacts complicates the use of automatic means of processing CT reconstruction results, such as segmentation, correction of geometric shapes, alignment of reconstructed volumes. Although there are numerous efficient methods for suppressing ring artifacts, many of them appear to be manual. Along with this, a large proportion of the automatic methods cope unsatisfactorily with the target task while requiring computational capacity. The current work introduces a projection data preprocessing method for suppressing ring artifacts that constitutes a compromise among the outlined aspects - automaticity, high efficiency and computational speed. Derived as the automation of the classical sinogram normalization method, the proposed method specific advantages consist in adaptability in relation to the filtered sinograms and the edge-preservation property proven within the experiments on both synthetic and real CT data. Concerning the challenging open-access data, the method has performed superior quality comparable to that of the advanced methods: it has demonstrated 70.4% ring artifacts suppression percentage (RASP) quality metric. In application to our real laboratory CT data, the proposed method allowed us to gain significant refinement of the reconstruction quality which has not been surpassed by a range of compared manual ring artifacts suppression methods.

Comparative study of calcification in human choroid plexus, pineal gland, and habenula

Choroid plexus, pineal gland, and habenula tend to accumulate physiologic calcifications (concrements) over a lifetime. However, until now the composition and causes of the intracranial calcifications remain unclear. The detailed analysis of concrements has been done by us using X-ray diffraction analysis (XRD), X-ray diffraction topography (XRDT), micro-CT, X-ray phase-contrast tomography (XPCT), as well as histology and immunohistochemistry (IHC). By combining physical (XRD) and biochemical (IHC) methods, we identified inorganic (hydroxyapatite) and organic (vimentin) components of the concrements. Via XPCT, XRDT, histological, and IHC methods, we assessed the structure of concrements within their appropriate tissue environment in both two and three dimensions. The study found that hydroxyapatite was a major component of all calcified depositions. It should be noted, however, that the concrements displayed distinctive characteristics corresponding to each specific structure of the brain. As a result, our study provides a basis for assessing the pathological and physiological changes that occur in brain structure containing calcifications.

X-ray Tomography Applied to Electrochemical Devices and Electrocatalysis

X-ray computed tomography (CT) is a nondestructive three-dimensional (3D) imaging technique used for studying morphological properties of porous and nonporous materials. In the field of electrocatalysis, X-ray CT is mainly used to quantify the morphology of electrodes and extract information such as porosity, tortuosity, pore-size distribution, and other relevant properties. For electrochemical systems such as fuel cells, electrolyzers, and redox flow batteries, X-ray CT gives the ability to study evolution of critical features of interest in ex situ, in situ, and operando environments. These include catalyst degradation, interface evolution under real conditions, formation of new phases (water and oxygen), and dynamics of transport processes. These studies enable more efficient device and electrode designs that will ultimately contribute to widespread decarbonization efforts.

Micromorphology of pineal gland calcification in age-related neurodegenerative diseases

BACKGROUND

The formation of concrements in human pineal gland (PG) is a physiological process and, according to many researchers, is associated with the involution of PG structures. The majority of scientific publications concern progressive calcification of PG, leaving out studies on the destruction of already formed calcified concrements. Our study fills the gap in knowledge about calcified zones destruction in PG in normal aging and neuropathological conditions, which has not been addressed until now.

PURPOSE

Our objective is to gain insight into human PG tissue impairment in both normal aging and neurodegenerative conditions. X-ray phase-contrast tomography (XPCT) allowed us to study PG tissue degeneration at high spatial resolution and, for the first time, to examine the damaged PG concrements in detail. Our research finding could potentially enhance the understanding of the PG involvement in the process of aging as well as in Alzheimer's disease (AD) and vascular dementia (VD).

METHODS

The research was carried out on human PG autopsy material in normal aging, VD, and AD conditions. Laboratory-based micro-computed tomography (micro-CT) was used to collect and evaluate samples of native, uncut, and unstained PG with different degrees of pineal calcification. The detailed high-resolution 3D images of the selected PGs were produced using synchrotron-based XPCT. Histology and immunohistochemistry of soft PG tissue confirmed XPCT results.

RESULTS

We performed via micro-CT the evaluation of the morphometric parameters of PG such as total sample volume, calcified concrements volume, and percentage of concrements in the total volume of the sample. XPCT imaging revealed high-resolution details of age-related PG alteration. In particular, we noted signs of moderate degradation of concrements in some PGs from elderly donors. In addition, our analysis revealed noticeable degenerative change in both concrements and soft tissue of PGs with neuropathology. In particular, we observed a hollow core and separated layers as well as deep ragged cracks in PG concrements of AD and VD samples. In parenchyma of some samples, we detected wide pinealocyte-free fluid-filled areas adjacent to the calcified zones.

CONCLUSION

The present work provides the basis for future scientific research focused on the dynamic nature of PG calcium deposits and PG soft tissue in normal aging and neurodegenerative diseases.

Image quality and scan time optimisation for in situ phase contrast x-ray tomography of the intervertebral disc

In-line phase contrast synchrotron tomography combined with in situ mechanical loading enables the characterisation of soft tissue micromechanics via digital volume correlation (DVC) within whole organs. Optimising scan time is important for reducing radiation dose from multiple scans and to limit sample movement during acquisition. Also, although contrasted edges provided by in-line phase contrast tomography of soft tissues are useful for DVC, the effect of phase contrast imaging on its accuracy has yet to be investigated. Due to limited time at synchrotron facilities, scan parameters are often decided during imaging and their effect on DVC accuracy is not fully understood. Here, we used previously published data of intervertebral disc phase contrast tomography to evaluate the influence of i) fibrous image texture, ii) number of projections, iii) tomographic reconstruction method, and iv) phase contrast propagation distance on DVC results. A greater understanding of how image texture influences optimal DVC tracking was obtained by visualising objective function mapping, enabling tracking inaccuracies to be identified. When reducing the number of projections, DVC was minimally affected by image high frequency noise but with a compromise in accuracy. Iterative reconstruction methods improved image signal-to-noise and consequently significantly lowered DVC displacement uncertainty. Propagation distance was shown to affect DVC accuracy. Consistent DVC results were achieved within a propagation distance range which provided contrast to the smallest scale features, where; too short a distance provided insufficient features to track, whereas too long led to edge effect inconsistencies, particularly at greater deformations. Although limited to a single sample type and image setup, this study provides general guidelines for future investigations when optimising image quality and scan times for in situ phase contrast x-ray tomography of fibrous connective tissues.

High-speed processing of X-ray wavefront marking data with the Unified Modulated Pattern Analysis (UMPA) model

Wavefront-marking X-ray imaging techniques use e.g., sandpaper or a grating to generate intensity fluctuations, and analyze their distortion by the sample in order to retrieve attenuation, phase-contrast, and dark-field information. Phase contrast yields an improved visibility of soft-tissue specimens, while dark-field reveals small-angle scatter from sub-resolution structures. Both have found many biomedical and engineering applications. The previously developed Unified Modulated Pattern Analysis (UMPA) model extracts these modalities from wavefront-marking data. We here present a new UMPA implementation, capable of rapidly processing large datasets and featuring capabilities to greatly extend the field of view. We also discuss possible artifacts and additional new features.

Pixel Image Analysis and Its Application with an Alcohol-Based Liquid Scintillator for Particle Therapy

We synthesized an alcohol-based liquid scintillator (AbLS), and we implemented an auxiliary monitoring system with short calibration intervals using AbLS for particle therapy. The commercial liquid scintillator used in previous studies did not allow the user to control the chemical ratio and its composition. In our study, the chemical ratio of AbLS was freely controlled by simultaneously mixing water and alcohol. To make an equivalent substance to the human body, 2-ethoxyethanol was used. There was no significant difference between AbLS and water in areal density. As an application of AbLS, the range was measured with AbLS using an electron beam in an image analysis that combined AbLS and a digital phone camera. Given a range-energy relationship for the electron expressed as areal density, the electron beam range (cm) in water can be easily estimated. To date, no literature report for the direct comparison of a pixel image analysis and Monte Carlo (MC) simulation has been published. Furthermore, optical tomography of the inverse problem was performed with AbLS and a mobile phone camera. Analyses of optical tomography images provide deeper insight into Radon transformation. In addition, the human phantom, which is difficult to compose with semiconductor diodes, was easily implemented as an image acquisition and analysis system.

3D Correlative Imaging of Lithium Ion Concentration in a Vertically Oriented Electrode Microstructure with a Density Gradient

The performance of Li+ ion batteries (LIBs) is hindered by steep Li+ ion concentration gradients in the electrodes. Although thick electrodes (≥300 µm) have the potential for reducing the proportion of inactive components inside LIBs and increasing battery energy density, the Li+ ion concentration gradient problem is exacerbated. Most understanding of Li+ ion diffusion in the electrodes is based on computational modeling because of the low atomic number (Z) of Li. There are few experimental methods to visualize Li+ ion concentration distribution of the electrode within a battery of typical configurations, for example, coin cells with stainless steel casing. Here, for the first time, an interrupted in situ correlative imaging technique is developed, combining novel, full-field X-ray Compton scattering imaging with X-ray computed tomography that allows 3D pixel-by-pixel mapping of both Li+ stoichiometry and electrode microstructure of a LiNi0.8 Mn0.1 Co0.1 O2 cathode to correlate the chemical and physical properties of the electrode inside a working coin cell battery. An electrode microstructure containing vertically oriented pore arrays and a density gradient is fabricated. It is shown how the designed electrode microstructure improves Li+ ion diffusivity, homogenizes Li+ ion concentration through the ultra-thick electrode (1 mm), and improves utilization of electrode active materials.

Nonuniqueness of hydrodynamic dispersion revealed using fast 4D synchrotron x-ray imaging

Experimental and field studies reported a significant discrepancy between the cleanup and contamination time scales, while its cause is not yet addressed. Using high-resolution fast synchrotron x-ray computed tomography, we characterized the solute transport in a fully saturated sand packing for both contamination and cleanup processes at similar hydrodynamic conditions. The discrepancy in the time scales has been demonstrated by the nonuniqueness of hydrodynamic dispersion coefficient versus injection rate (Péclet number). Observations show that in the mixed advection-diffusion regime, the hydrodynamic dispersion coefficient of cleanup is significantly larger than that of the contamination process. This nonuniqueness has been attributed to the concentration-dependent diffusion coefficient during the cocurrent and countercurrent advection and diffusion, present in contamination and cleanup processes. The new findings enhance our fundamental understanding of transport processes and improve our capability to estimate the transport time scales of chemicals or pollution in geological and engineering systems.

Tomosipo: fast, flexible, and convenient 3D tomography for complex scanning geometries in Python

Tomography is a powerful tool for reconstructing the interior of an object from a series of projection images. Typically, the source and detector traverse a standard path (e.g., circular, helical). Recently, various techniques have emerged that use more complex acquisition geometries. Current software packages require significant handwork, or lack the flexibility to handle such geometries. Therefore, software is needed that can concisely represent, visualize, and compute reconstructions of complex acquisition geometries. We present tomosipo, a Python package that provides these capabilities in a concise and intuitive way. Case studies demonstrate the power and flexibility of tomosipo.